Variant report

Variant	rs3754418
Chromosome Location	chr1:227348473-227348474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10799381	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916080	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916104	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12039370	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139758	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1320494	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1483	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929858	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2102634	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2482454	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2492630	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670462	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2670471	0.80[AMR][1000 genomes]
rs2718193	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2813950	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2813965	0.80[AMR][1000 genomes]
rs2813969	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2813970	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4351610	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653479	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485234	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488104	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56219094	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648877	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662583	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6682472	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6682642	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692080	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6697665	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6699828	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689094	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs694740	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7412928	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7512409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7521110	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7521639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7523167	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7543579	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7549520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
2	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
5	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:227316600-227352200	Weak transcription	Gastric	stomach
7	chr1:227317000-227374200	Weak transcription	HepG2	liver
8	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
9	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:227328400-227350000	Weak transcription	Fetal Brain Male	brain
11	chr1:227328600-227351600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
15	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:227332800-227350000	Weak transcription	HMEC	breast
18	chr1:227332800-227350200	Weak transcription	Lung	lung
19	chr1:227332800-227354600	Weak transcription	Ovary	ovary
20	chr1:227333000-227349400	Weak transcription	Placenta	Placenta
21	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:227333400-227354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:227333400-227354400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:227333400-227358400	Weak transcription	Osteobl	bone
25	chr1:227333400-227359000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
28	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:227339600-227354000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:227343200-227350600	Weak transcription	Stomach Mucosa	stomach
31	chr1:227343200-227352400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:227343200-227400400	Weak transcription	A549	lung
33	chr1:227343600-227358400	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:227346200-227348800	Strong transcription	K562	blood
35	chr1:227346800-227349800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:227346800-227350000	Weak transcription	Pancreas	Pancrea
37	chr1:227346800-227351200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:227346800-227354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:227346800-227355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:227346800-227357400	Weak transcription	Brain Substantia Nigra	brain
41	chr1:227346800-227357800	Weak transcription	NHDF-Ad	bronchial
42	chr1:227346800-227358000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:227346800-227358200	Weak transcription	Right Ventricle	heart
44	chr1:227346800-227358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227346800-227366600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
50	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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